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. 2010 Jul;38(Web Server issue):W138-43.
doi: 10.1093/nar/gkq318. Epub 2010 Apr 30.

PathPred: an enzyme-catalyzed metabolic pathway prediction server

Yuki Moriya  1 , Daichi Shigemizu, Masahiro Hattori, Toshiaki Tokimatsu, Masaaki Kotera, Susumu Goto, Minoru Kanehisa
Affiliations

PathPred: an enzyme-catalyzed metabolic pathway prediction server

Yuki Moriya et al. Nucleic Acids Res. 2010 Jul.

Abstract

The KEGG RPAIR database is a collection of biochemical structure transformation patterns, called RDM patterns, and chemical structure alignments of substrate-product pairs (reactant pairs) in all known enzyme-catalyzed reactions taken from the Enzyme Nomenclature and the KEGG PATHWAY database. Here, we present PathPred (http://www.genome.jp/tools/pathpred/), a web-based server to predict plausible pathways of muti-step reactions starting from a query compound, based on the local RDM pattern match and the global chemical structure alignment against the reactant pair library. In this server, we focus on predicting pathways for microbial biodegradation of environmental compounds and biosynthesis of plant secondary metabolites, which correspond to characteristic RDM patterns in 947 and 1397 reactant pairs, respectively. The server provides transformed compounds and reference transformation patterns in each predicted reaction, and displays all predicted multi-step reaction pathways in a tree-shaped graph.

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Figures

Figure 1.
Figure 1.
The protocol of PathPred.
Figure 2.
Figure 2.
The example of the predicted pathway tree of tetrachlorobenzene biodegradation (A) and the detail of the top green pathway from the query compound (Query) to the final compound (C00160) (B). Structure images popup when the mouse is moved over nodes and edges in the tree if JavaScript is enabled in the web browser.
Figure 3.
Figure 3.
An example of the predicted reactions.
Figure 4.
Figure 4.
The example of the predicted pathway tree of gentiodelpin biosynthesis (A) and the structure of gentiodelpin (B).
See this image and copyright information in PMC

References

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